O.K., so here is the idea I had. It may not quite work with the overall CA route scheme you gave. CA is a large state. Upon leaving SF, Yosemite is 5+ hours away. Some of these places on the southeast side of the Sierra would take a full day to reach from SF. Just about the closest place in the Sierra from SF is Lake Tahoe, which is 4 hours away. If you were to combine your 1 night backpack trip with a stop at Tahoe, you could maximize some time in 1 location. This is the area I mentioned in my earlier post. I would recommend a 2 night trip into Desolation Wilderness, starting at Echo Lake. Take the ferry from the dam to the upper end of Upper Echo Lake and spend the first night at Lake Aloha, a sizeable alpine lake with numerous islands with the impresive Crystal Range and Pyramid Peak reflected in the water from the other side. On the second day, you'd hike 8 miles to Lake GIlmore, set camp, then climb Mt. Tallac from whose summit you look straight down from heaven upon mountain encircled azure blue Lake Tahoe which is 72 mi. in circumference. From there, you head back to camp. In the morning, it's a brisk 2-2.5 hours to the trailhead at Glen Alpine Spring and out via beautiful Fallen Leaf Lake.

Now that scenario involves hitching or arranging an extra vehicle for aways. There is a way to do most of this as a loop, but there's a little more elevation change and you skip the ferry boat. This way is to begin at Glen Alpine and make the climb to Gilmore, set camp, climb Tallac, come back, camp. Day 2, go to Aloha, last day, exit via the Angora Ridge Trail back to Lily Lake, which is really close to Glen Alpine.

If you are really fit and like covering miles, you might be able to do all this in two full days and one night out. When you exit, you'd already be at Tahoe where you can enjoy many other beautiful opportunities of your vacation. And as I said previously, the elevation is high enough that parts are alpine (above tree line), but with most of it around 8000', you're not going to have the kind of altitude problems you might incur in the Whitney area around 14,000'. The one thing you should know is that Desolation is relatively small and popular, so there will be no sense of solitude, but then again, you're less likely to find that anywhere if you're only one night in.

Here is a link to a map of the area I've suggested. Ignore the side treks I have to Lake of the Woods, etc.

Since you want to visit Yosemite Valley and then drive on to Zion National Park, 20 Lakes Basin is a natural. It is on the way from YV to ZNP. It starts at altitude so you won't "waste" time huffing and puffing your way up hill. The scenery is excellent (most years anyway). You can drop by the Wilderness Permit Office in YV the day before and grab a walk-up (unreserved) permit. (Note: have a plan B & C). The only downside is that it is a popular loop so don't expect solitude.

Since 20 Lakes Basin doesn't require much driving perhaps you can day hike YV and Tuolumne Meadows an extra day and then start your backpack on a a Monday (no worry of permit quotas), or take an extra day for the backpack trip and climb a peak like Mt Conness.

Sorry you had to see the waterfalls in a major drought year. Perhaps you can return in the future for a big Spring runnoff.

If you like the idea of Thousand Island Lake, I think it could fit neatly into your plans as you describe them.

On your first travel day, you could head from San Francisco to Yosemite Valley, see the sights there, then head across the Sierra via Tioga Road, with a few sightseeing stops. Once you cross the mountains, you could check out Mono Lake, if you have time, and then grab a campsite somewhere in the area (June Lake?).

The next morning, you could get up early and head to the trailhead. As someone mentioned, if you want to drive to the Agnew Meadows trailhead, you have to be there by 7 AM. Otherwise, you can park your car and take the shuttle to the trailhead. I did the exact loop you described two years ago, albeit in the opposite direction. The first day (Agnew -> Shadow -> Garnet -> Thousand Island) is a bit longer. I hiked with two folks who were not the strongest hikers I've ever met. We hit the trail around 10:30 and got to Thousand Island around dusk. It would certainly be possible to hike this portion of the loop more quickly. The second day, I took the High Trail back to Agnew Meadows solo. It didn't take me long at all-- I think I was on the shuttle bus back to town by noon. If you are reasonably strong hikers, this loop should be no problem at all.

Of course, many of the options that others have described are beautiful as well. Lots to see.

You can check the photo and see if the falls are still flowing when you plan your trip.

I agree that 20 Lakes is a good choice. I feel Conness Lake is the most scenic, but it is a day-use only area - have to camp at Cascade Lake. Although an overnight trip to Island Lake or Iceberg Lake out of Agnew Meadows would be more scenic, I have never found the required public transportation very efficient You will likely loose an hour or two just to get where you want to go to start hiking and get back to your car. If I were pressed for time, the crowds and hassles would get me annoyed. If you go down 395 and through Bishop, an overnight out of South Lake or Lake Sabrina is very scenic from the first step on the trail. There are numerous campgrounds all the way up the road to the trailheads. The trailheads (South Lake or Sabrina Lake) are about 20 minutes from Bishop.

If you like the idea of Thousand Island Lake, I think it could fit neatly into your plans as you describe them.

On your first travel day, you could head from San Francisco to Yosemite Valley, see the sights there, then head across the Sierra via Tioga Road, with a few sightseeing stops. Once you cross the mountains, you could check out Mono Lake, if you have time, and then grab a campsite somewhere in the area (June Lake?).

The next morning, you could get up early and head to the trailhead. As someone mentioned, if you want to drive to the Agnew Meadows trailhead, you have to be there by 7 AM. Otherwise, you can park your car and take the shuttle to the trailhead. I did the exact loop you described two years ago, albeit in the opposite direction. The first day (Agnew -> Shadow -> Garnet -> Thousand Island) is a bit longer. I hiked with two folks who were not the strongest hikers I've ever met. We hit the trail around 10:30 and got to Thousand Island around dusk. It would certainly be possible to hike this portion of the loop more quickly. The second day, I took the High Trail back to Agnew Meadows solo. It didn't take me long at all-- I think I was on the shuttle bus back to town by noon. If you are reasonably strong hikers, this loop should be no problem at all.

Of course, many of the options that others have described are beautiful as well. Lots to see.

Thanks for all the info. I think I will zero in on this...know there are tons of good options, but seems to fit well with what I had hoped to do and is more or less on our way in terms of our trip.

I looked into camping at Agnew Meadows and saw that the campground is closed because of a bad windstorm. Is this going to adversely affect our hike in any way?

Papercup, did you use the Shadow Lake trailhead on your hike? It looks like that would be what I would want to reserve if I did a trip similar to what you describe...

It looks like June Lake Campground is full for the night we would need. I think we'd probably be arriving too late to rely on a walk-up. Is there another campground anyone could recommend that would be on our route from Yosemite Valley to Agnew Meadows?

The windstorm destroyed the Agnew campground, but the trails have all been cleared and it won't have an impact on your hike.

Shadow Creek is the permit that I used, although you can also access Thousand Island via the River Trail or High Trail. If you take the High Trail to Thousand Island, you're going to do almost all of your climbing right at the beginning, and then cruise along after that. The Shadow Creek route is a bit more varied. I haven't been down the River Trail, so can't comment.

There should be a number of campgrounds between Lee Vining and Mammoth. I can't say that I'm super familiar with many of them. I've stayed at the Oh Ridge campground, close to June Lake, but that's really all I know. I'm sure there are more. Probably not a bad idea to try to stay at the highest elevation campground that seems reasonable.

Looking at the permit page for the Agnew Meadows area, it looks like road access to the trailhead only starts in late June. It seems like you should be OK this year, given the low snow, but that is probably something worth looking into a bit.

It doesn't take 5 hours to get to Yosemite Valley from SF. It's more like 3.5. I'm actually about to do it tomorrow morning! Also, driving to the Agnew trailhead is impossible unless you arrive in Mammoth the day before---you have to pick up a permit from the ranger and they open later than the road closes. As far as what's the best route to hike, it kinda depends on what you like. The River Trail in the valley there is heavily forested and monotonous while the High Trail is exposed, out in the open, with major megaviews the whole way basically (can you tell what I like? )

Depending on exactly how many days you have, I'd suggest something like what's been suggested before:

Day 1: Leave SF as early as possible. If you leave by 6am or so, you'll be in Yosemite by 10am latest. (You're headed opposite of commute traffic. Yay!) I'd head in via the 140 and check out the Mariposa Grove and Glacier Point before driving down into the valley. Drive around the valley with one million billion other people who booked their trips five months ago and are super bummed about the small waterfalls this year due to 30% of average snowpack. Don't bother hiking anywhere, but do see what you can see from the valley and pullouts. Around 4pm, head out of the valley and drive along Tioga Road to the east. This will give you enough light to see some stuff as you drive east. Head to Mammoth Lakes and camp in one of the Shady Rest campgrounds.

Day 2: Pick up your permit from the ranger in the morning and take the shuttle to the Agnew trailhead. Hike the High Trail in to Thousand Island lake. Camp. The sunrise and sunsets at Thousand Island are super nice. Then hike out however you want. If start early and take the JMT to Shadow Lake to the River trail to Agnew (about 8-9 miles), I think you can be back at your car in time to get a couple hours of driving in before shacking up at a motel in BFE.

Day 3: Drive to Zion. You can probably be there by early afternoon, so you have time to check some stuff out around the canyon and sign up for everything for the Narrows trip the next day. It's an amazing, truly unique, experience. I did it as an overnight 8 or so years back. Backpacking up the West Rim trail is super rad also.

It doesn't take 5 hours to get to Yosemite Valley from SF. It's more like 3.5. I'm actually about to do it tomorrow morning! Also, driving to the Agnew trailhead is impossible unless you arrive in Mammoth the day before---you have to pick up a permit from the ranger and they open later than the road closes. As far as what's the best route to hike, it kinda depends on what you like. The River Trail in the valley there is heavily forested and monotonous while the High Trail is exposed, out in the open, with major megaviews the whole way basically (can you tell what I like? )

Depending on exactly how many days you have, I'd suggest something like what's been suggested before:

Day 1: Leave SF as early as possible. If you leave by 6am or so, you'll be in Yosemite by 10am latest. (You're headed opposite of commute traffic. Yay!) I'd head in via the 140 and check out the Mariposa Grove and Glacier Point before driving down into the valley. Drive around the valley with one million billion other people who booked their trips five months ago and are super bummed about the small waterfalls this year due to 30% of average snowpack. Don't bother hiking anywhere, but do see what you can see from the valley and pullouts. Around 4pm, head out of the valley and drive along Tioga Road to the east. This will give you enough light to see some stuff as you drive east. Head to Mammoth Lakes and camp in one of the Shady Rest campgrounds.

Day 2: Pick up your permit from the ranger in the morning and take the shuttle to the Agnew trailhead. Hike the High Trail in to Thousand Island lake. Camp. The sunrise and sunsets at Thousand Island are super nice. Then hike out however you want. If start early and take the JMT to Shadow Lake to the River trail to Agnew (about 8-9 miles), I think you can be back at your car in time to get a couple hours of driving in before shacking up at a motel in BFE.

Day 3: Drive to Zion. You can probably be there by early afternoon, so you have time to check some stuff out around the canyon and sign up for everything for the Narrows trip the next day. It's an amazing, truly unique, experience. I did it as an overnight 8 or so years back. Backpacking up the West Rim trail is super rad also.

This is great info, especially about what kind of scenery we should expect along the High Trail and River Trail. Do you know if the JMT in that area is more similar to the High Trail (exposed) or River Trail (forested)? I do want to use the JMT either going in or coming out, so I'd probably decide on either the High Trail or River Trail based on what was going to give us the most diverse experience.